使用列名称向量将数据框的多个列（如对象）提取并粘贴在一起

I have an object (variable rld) which looks a bit like a "data.frame" (see further down the post for details) in that it has columns that can be accessed using $ or [[]].

我有一个对象（变量rld）看起来有点像“data.frame”（详见帖子下面的详细信息），因为它有可以使用$或[[]]访问的列。

I have a vector groups containing names of some of its columns (3 in example below).

我有一个包含其某些列名称的向量组（下面的示例中为3）。

I generate strings based on combinations of elements in the columns as follows:

我根据列中元素的组合生成字符串，如下所示：

paste(rld[[groups[1]]], rld[[groups[2]]], rld[[groups[3]]], sep="-")

I would like to generalize this so that I don't need to know how many elements are in groups.

我想概括一下，这样我就不需要知道组中有多少元素了。

The following attempt fails:

以下尝试失败：

> paste(rld[[groups]], collapse="-")
Error in normalizeDoubleBracketSubscript(i, x, exact = exact, error.if.nomatch = FALSE) : 
  attempt to extract more than one element

Here is how I would do in functional-style with a python dictionary:

以下是我将如何使用python字典进行功能样式：

map("-".join, zip(*map(rld.get, groups)))

Is there a similar column-getter operator in R ?

R中是否有类似的列-getter运算符？

As suggested in the comments, here is the output of dput(rld): http://paste.ubuntu.com/23528168/ (I could not paste it directly, since it is huge.)

正如评论中所建议的，这里是dput（rld）的输出：http：//paste.ubuntu.com/23528168/（我无法直接粘贴它，因为它很大。）

This was generated using the DESeq2 bioinformatics package, and more precisely, doing something similar to what is described page 28 of this document: https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf.

这是使用DESeq2生物信息学软件包生成的，更准确地说，是与本文档第28页所描述的类似：https：//www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/ DESeq2.pdf。

DESeq2 can be installed from bioconductor as follows:

DESeq2可以从bioconductor安装如下：

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

Reproducible example

One of the solutions worked when running in interactive mode, but failed when the code was put in a library function, with the following error:

其中一个解决方案在交互模式下运行时有效，但在将代码放入库函数时失败，出现以下错误：

Error in do.call(function(...) paste(..., sep = "-"), colData(rld)[groups]) : 
  second argument must be a list

After some tests, it appears that the problem doesn't occur if the function is in the main calling script, as follows:

经过一些测试后，如果函数在主调用脚本中，似乎不会出现问题，如下所示：

library(DESeq2)
library(test.package)

lib_names <- c(
    "WT_1",
    "mut_1",
    "WT_2",
    "mut_2",
    "WT_3",
    "mut_3"
)
file_names <- paste(
    lib_names,
    "txt",
    sep="."
)

wt <- "WT"
mut <- "mut"
genotypes <- rep(c(wt, mut), times=3)
replicates <- c(rep("1", times=2), rep("2", times=2), rep("3", times=2))

sample_table = data.frame(
    lib = lib_names,
    file_name = file_names,
    genotype = genotypes,
    replicate = replicates
)

dds_raw <- DESeqDataSetFromHTSeqCount(
    sampleTable = sample_table,
    directory = ".",
    design = ~ genotype
    )

# Remove genes with too few read counts
dds <- dds_raw[ rowSums(counts(dds_raw)) > 1, ]
dds$group <- factor(dds$genotype)
design(dds) <- ~ replicate + group
dds <- DESeq(dds)

test_do_paste <- function(dds) {
    require(DESeq2)
    groups <- head(colnames(colData(dds)), -2)
    rld <- rlog(dds, blind=F)
    stopifnot(all(groups %in% names(colData(rld))))
    combined_names <- do.call(
        function (...) paste(..., sep = "-"),
        colData(rld)[groups]
    )
    print(combined_names)
}

test_do_paste(dds)
# This fails (with the same function put in a package)
#test.package::test_do_paste(dds)

The error occurs when the function is packaged as in https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/

函数打包时出现错误，如https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/

Data used in the example:

示例中使用的数据：

WT_1.txt

WT_1.txt
WT_2.txt

WT_2.txt
WT_3.txt

WT_3.txt
mut_1.txt

mut_1.txt
mut_2.txt

mut_2.txt
mut_3.txt

mut_3.txt

I posted this issue as a separate question: do.call error "second argument must be a list" with S4Vectors when the code is in a library

我把这个问题作为一个单独的问题发布了：当代码在库中时，do.call错误“第二个参数必须是一个列表”与S4Vectors

Although I have an answer to my initial question, I'm still interested in alternative solutions for the "column extraction using a vector of column names" issue.

虽然我对最初的问题有答案，但我仍然对“使用列名称向量列提取”问题的替代解决方案感兴趣。

1 个解决方案

#1

We may use either of the following:

我们可能会使用以下任何一种方法：

do.call(function (...) paste(..., sep = "-"), rld[groups])
do.call(paste, c(rld[groups], sep = "-"))

We can consider a small, reproducible example:

我们可以考虑一个小的，可重现的例子：

rld <- mtcars[1:5, ]
groups <- names(mtcars)[c(1,3,5,6,8)]
do.call(paste, c(rld[groups], sep = "-"))
#[1] "21-160-3.9-2.62-0"     "21-160-3.9-2.875-0"    "22.8-108-3.85-2.32-1" 
#[4] "21.4-258-3.08-3.215-1" "18.7-360-3.15-3.44-0"

Note, it is your responsibility to ensure all(groups %in% names(rld)) is TRUE, otherwise you get "subscript out of bound" or "undefined column selected" error.

注意，您有责任确保所有（％名称（rld）中的组％）为TRUE，否则会出现“下标超出范围”或“未定义列选择”错误。

(I am copying your comment as a follow-up)

（我正在复制你的评论作为后续行动）

It seems the methods you propose don't work directly on my object. However, the package I'm using provides a colData function that makes something more similar to a data.frame:

看来你提出的方法不能直接在我的对象上工作。但是，我正在使用的包提供了一个colData函数，它使一些更类似于data.frame：

> class(colData(rld))
[1] "DataFrame"
attr(,"package")
[1] "S4Vectors"

do.call(function (...) paste(..., sep = "-"), colData(rld)[groups]) works, but do.call(paste, c(colData(rld)[groups], sep = "-")) fails with an error message I fail to understand (as too often with R...):

do.call（function（...）paste（...，sep =“ - ”），colData（rld）[groups]）有效，但是do.call（paste，c（colData（rld）[groups]， sep =“ - ”））失败并显示错误消息我无法理解（通常使用R ...）：

> do.call(paste, c(colData(rld)[groups], sep = "-"))
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘mcols’ for signature ‘"character"’

#1